De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages

BMC Genomics

Table 1 Assembly and annotation statistics for the combined assembly containing all three tissues and four growth stages along with individual assemblies for the seven tissue/growth stages of A. spica-venti

	Seed 05	Seed 07	Seed 08	Seed 09	Leaf	Root	Stem	All tissues
Surviving Paired Reads	33,047,108	34,553,732	35,507,768	34,083,440	27,518,992	47,701,648	28,792,480	241,205,168
Transcript number before rr^a	2,300,488	319,916	284,019	266,532	149,469	222,747	117,629	669,871
Transcripts number after rr^a	41,963	45,511	43,324	47,423	32,001	46,168	33,244	83,349
Genes	38,088	42,292	40,042	43,316	28,246	38,972	28,513	74,724
Total bases	33,259,794	31,598,526	31,320,780	34,985,208	24,432,147	36,146,334	29,060,739	54,846,111
GC %	53	53	53	53	52	53	53	53
Number of protein coding transcripts
> = 1 kbp	9,887	8,024	8,628	9,873	7,207	10,922	9,803	13,019
Max contig lenght	11,865	10,923	11,733	9,633	11,736	14,148	12,282	14,247
average contig lenght	776	694	722	737	763	782	874	658
N50	999	834	900	927	966	1,017	1143	762
N50 longest isoform	1,038	849	915	951	1,014	1,098	1,218	783
BLASTp:
hit % B. distachyon	97	98	98	97	98	97	98	97
hit % Uniprot	96	96	97	96	96	95	96	94
% GO mapped	72	73	74	74	75	74	73	73
% functionally annotated	56	58	58	56	62	55	58	50

^arr; redundancy reduction steps (after the Trinity de novo assembly). Surviving paired reads represents paired reads remaining after the quality control and normalization steps
Similar to the individual assemblies, the combined dataset has 10,163 sequences that have an enzyme code representing 12% of the total transcript number. The e-values distribution of the combined assembly shows the 78% of transcripts with an e-value of <1e⁻¹⁰ (Additional file 2) indicating high confidence in the annotation performed

ISSN: 1471-2164